Smart UV project creates overlapping uv-coordinates
Smart UV Project simply doesn't guarantee non-overlapping UVs.

It doesn't detect or correct self-intersecting UV's within a UV-island.

Using lower angle limit will typically help to avoid this problem, but there are still cases it could happen.

If the possibility of overlapping UV's is unacceptable, you could use Lightmap-pack instead.



Note, in the example given - there is a lot of noise, One way to resolve could mitigate overlapping could be calculate the UV's on a less noisy version of the mesh:


Store the original vertex locations.
Smooth the vertices.
Execute Smart-Project
Restore the vertex locations.